Figure 1

Chikungunya virus is found in MARCO-expressing floor lymphatic endothelial cells in the draining lymph node at 8 hpi


Figure S1

CHIKV may target MARCO-expressing LECs for infection

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Version 2


Figure 5

CHIKV infection induces distinct cell type-specific gene expression programs

A. The average fold change in expression is shown below for the top 6 CHIKV-induced gene expression programs. Fold changes were scaled and centered for each gene (row). A darker tile indicates the gene is more strongly upregulated in the cell type (e.g. the Marco LEC cluster includes genes that are generally more highly upregulated in Marco LECs)

B. The top 6 gene ontology terms are shown for the gene expression programs described in A.

C. Select genes identified in A are shown below for mock- and CHIKV-infected samples. p-values comparing mock- and CHIKV-infected samples are shown above each set of boxplots.

Brief description of approach:

  1. Upregulated genes for each cell type were identified by comparing mock- and CHIKV-infected samples. To be included, a gene must have an adjusted p-value <0.05 for all replicates and >1.25 fold increase in expression for all replicates.
  2. Hierarchical clustering was used to divide upregulated genes into 10 groups based on their average fold change in expression for each cell type.
  3. The top 7 clusters are shown below. The top 2 clusters (based on number of genes) appeared functionally similar and were merged into one cluster (interferon response).